As best I can tell, youtube is using the 'moovposition' metadata property embedded in the MPEG-4 container file to determine where the seek bar should be. When a 'seek' is performed, youtube downloads a new movie file which would have a different moovposition.

Apparently onMetaData gets exposed this information from the MPEG-4 metadata, according to:

It seems that with these videos youtube plays from a new NetStream URL when a seek is attempted. It seems to me that Gnash accurately reports the position in the new file that's downloaded, which would be why the time bar indicator moves to the start position.